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Detailed information for vg0122343655:

Variant ID: vg0122343655 (JBrowse)Variation Type: SNP
Chromosome: chr01Position: 22343655
Reference Allele: CAlternative Allele: A
Primary Allele: CSecondary Allele: A

Inferred Ancestral Allele : C (evidence from allele frequency in Oryza rufipogon: C: 0.74, A: 0.27, others allele: 0.00, population size: 200. )

Flanking Sequence (100 bp) in Reference Genome:


TACTACAGAACAATAAAAAATATATGGTTTTTGCTAGCAGACACTTGAATTTATATAAGGACATTAAAAAAAATAGTAATTTGCCACATGACATCGTGAA[C/A]
AGTAAAATACAATATTCACTTAGTTGGGAAGAGAAAAACCACGTCAAATAACCATTTTACCCTAATATTCTTCTCCCTATTTTCCTCCTCAACGGGTTGT

Reverse complement sequence

ACAACCCGTTGAGGAGGAAAATAGGGAGAAGAATATTAGGGTAAAATGGTTATTTGACGTGGTTTTTCTCTTCCCAACTAAGTGAATATTGTATTTTACT[G/T]
TTCACGATGTCATGTGGCAAATTACTATTTTTTTTAATGTCCTTATATAAATTCAAGTGTCTGCTAGCAAAAACCATATATTTTTTATTGTTCTGTAGTA

Allele Frequencies:

Populations Population SizeFrequency of C(primary allele) Frequency of A(secondary allele) Frequency of N Frequency of DEL Frequency of others Allele
All  4726 54.50% 45.40% 0.02% 0.00% NA
All Indica  2759 30.50% 69.40% 0.04% 0.00% NA
All Japonica  1512 99.60% 0.40% 0.00% 0.00% NA
Aus  269 60.60% 39.40% 0.00% 0.00% NA
Indica I  595 0.70% 99.30% 0.00% 0.00% NA
Indica II  465 29.20% 70.80% 0.00% 0.00% NA
Indica III  913 47.80% 52.10% 0.11% 0.00% NA
Indica Intermediate  786 33.80% 66.20% 0.00% 0.00% NA
Temperate Japonica  767 100.00% 0.00% 0.00% 0.00% NA
Tropical Japonica  504 99.60% 0.40% 0.00% 0.00% NA
Japonica Intermediate  241 98.30% 1.70% 0.00% 0.00% NA
VI/Aromatic  96 10.40% 89.60% 0.00% 0.00% NA
Intermediate  90 63.30% 36.70% 0.00% 0.00% NA

Allele Effect:

Var ID Var Locus snpEff Annotation CooVar Annotation Chromatin Accessibility Score PolyPhen-2 Effect PolyPhen-2 Score SIFT Effect SIFT Score
vg0122343655 C -> A LOC_Os01g39600.1 upstream_gene_variant ; 2177.0bp to feature; MODIFIER silent_mutation Average:83.386; most accessible tissue: Zhenshan97 panicle, score: 94.36 N N N N
vg0122343655 C -> A LOC_Os01g39600.2 upstream_gene_variant ; 2110.0bp to feature; MODIFIER silent_mutation Average:83.386; most accessible tissue: Zhenshan97 panicle, score: 94.36 N N N N
vg0122343655 C -> A LOC_Os01g39600-LOC_Os01g39630 intergenic_region ; MODIFIER silent_mutation Average:83.386; most accessible tissue: Zhenshan97 panicle, score: 94.36 N N N N

Effects Predicted by Deep Convolutional Neural Networks

For each variant, we constructed two sequences that contain the variation site and the sequence around it, differing only in the variation site. We then used Basenji to predict the chromatin accessibility of each tissue for the two sequences, respectively, and scored the effect of the variant by comparing the changes in chromatin accessibility corresponding to the two genotypes in the 1 kb region around the variation site. The effect score was defined as the logarithmic ratio of the predicted chromatin accessibility of the alternative genotype to the value of the reference genotype.

Var ID Ref Alt Root (RT) Young Leaf (YL) Flag Leaf (FL) Young Panicle (YP) Lemma & Palea (LP) Stamen & Pistil (SP)
vg0122343655 C A 0.01 0.01 0.01 0.0 0.02 0.02

Putative Genotype-Phenotype Associations:

Var ID LMM P-value LR P-value Trait Subpopulation Is leadSNP Publication
vg0122343655 3.32E-06 NA mr1015 Ind_All YES Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 5.55E-08 mr1080 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 4.47E-06 mr1100 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 9.33E-07 mr1124 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 3.58E-06 mr1203 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 2.24E-08 mr1613 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 9.70E-07 mr1618 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 3.33E-07 mr1861 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 4.13E-11 mr1962 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 8.85E-08 mr1619_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 8.68E-09 mr1795_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 5.26E-06 mr1888_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 4.61E-09 mr1946_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 4.61E-09 mr1948_2 All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251
vg0122343655 NA 3.52E-09 mr1962_2 Ind_All Not Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251